You Chose Her
by SherlockiansGetBored
Summary: This is a story I wrote based on BeautifullyTragic6's amazing Series 4 promo "Detective vs Assassin". Mary Watson's past is not entirely behind her. (Hints of Sherlolly.)
1. Chapter 1

**A/N: Thank you so much to BeautifullyTragic6 for making the trailer that inspired this fic and for allowing me to post this story. It does not do justice to her amazing video: Sherlock Series 4 Promo #4: "Detective VS Assassin", and her amazing video editing skills. This chapter marks seven days until Sherlock Series 4. SERIES 4 SPOILER WARNING: This story does use the confirmed name of John and Mary's baby.**

Chapter 1:

It had been a year since John Watson had forgiven his wife Mary for lying to him about her past life as an assassin. The Watsons had made up just in time to start preparing to become parents for the first time. They chose to name their baby daughter Rosamund Mary Watson, Rosie for short.

John struggled to hold onto the screaming baby as Mary gathered all of the things that Sherlock would need to take care of her before he arrived. He and Molly were babysitting for the day because both John and Mary had to work. Usually Mary and John would try to alternate days, but Mary was called in to work at the last minute.

There was a knock at the door just as John handed Rosie off to Mary. John answered the door while Mary set Rosie down in her play pen.

"Hi, John," said Molly with a cheery smile on her face. She waved at Rosie who was now sitting calmly and happily.

"Hello, come in," John said. He opened the door allowing Molly to enter. She was followed by Sherlock who did not look happy to be there.

"Lighten up, Sherlock," said Mary. "I thought you were starting to get attached to Rosie."

"I was busy with a case," Sherlock replied quickly.

"I'm not John. I know when you're fibbing," Mary said with a knowing smile.

"Don't worry, Mary. He's happy to be here, even if he won't admit it," said Molly.

Molly walked over to see the baby. "Hello, Rosie. Do you remember me? Aunty Molly?" Rosie laughed, reaching up to grab on of Molly's hair that hung over the edge of the pen.

"Well, we should be going. I'm sure you guys have everything under control," said John. This was the third time that Sherlock and Molly had come over to babysit.

"All of Rosie's stuff is right here," Mary said, pointing to a care bag she had put together. "I just have to check on something. Back in a second." She quickly left the room to go upstairs.

"Thanks again for doing this, Molly," John said.

"It's no problem. I wanted to," she said. "Besides, I'll make sure that Sherlock is kept busy this time."

"Alright, shall we go then?" said Mary as she came back downstairs.

John led the way out the door. "We'll be back before six. Take care of him," Mary said, winking at Molly.

"I will," Molly said, smiling back at Mary. "Say bye bye, Rosie."

Once John and Mary were gone, Molly turned to Sherlock who was sitting on the couch, checking his phone. "If we have until 6:00, that means we're here for a full…" She glanced at the clock in the kitchen. 8:00. "…ten hours."

"Bored. I could solve 3 cases in that time," Sherlock said.

"Well, you aren't going to. You are going to help me take care of Rosie," Molly said.

"Fine," Sherlock sighed. He jumped up from the couch and walked to where Molly was standing.

They both spent the next couple hours playing with the baby, feeding her and changing her diapers. After Sherlock and Molly had made lunch for themselves and Rosie had settled down for a nap, they both sat down to take a break. Sherlock sat back down on the couch where he had been sitting before, and Molly took a seat in the armchair to the right of him.

Eventually, Molly tucked her feet up on the chair and fell asleep. Once Sherlock had finished filing away a few things about babysitting into his mind palace, he decided to have a look around the flat. It would be interesting to see what the Watsons' life was like when he wasn't around.

He immediately came across a room at the top of the stairs that was locked. He found the key under a small angel statue sitting on a small table in the hall beside the door. Inside there was a filing cabinet in one corner, a potted plant in another corner, a desk against one wall with a wooden box beside it that had a door on the front, and a wardrobe on the opposite wall.

Sherlock walked over to examine the wooden box. The door on it was locked. He noticed a stool next to the wardrobe which he assumed was used to reach items on top of it. He was tall enough reach his hand up and feel the top of the wardrobe without it. He felt the cold metal of a key and took it down to see if it would fit into the lock on the wooden box. It was no surprise that it fit perfectly. The lock clicked open.

Sherlock sighed when he saw that there was yet another lock on a small file box inside. What was with all of this secrecy? This time, it was a padlock with a four letter code. This brought back memories of his case with Miss Adler, the woman. The woman. He started to become distracted with his memories, but quickly focused himself to solve the task at hand.

It was clearly stated on the file box: Property of Mary Watson. He needed to figure out the four letter code. What could it be? Sherlock decided to start off having a bit of fun. Maybe Mary was as sentimental as Miss Adler had been. He put in the combination J-O-H-N. He tried the lock, but it wouldn't move.

 _I guess she wouldn't choose something that obvious. This much protection must be for something important_ , Sherlock thought. He chuckled to himself. _Could she really be self-centered enough to make it—_

M-A-R-Y. No luck.

There was no time for games now. He wanted to solve this case that he had brought upon himself before either the baby or Molly woke up. He needed to think. What code would Mary choose that even John would not guess? What would be something important to her? Then it came to him. He remembered the day that he had discovered her secret.

A-G-R-A.

Her initials. The lock clicked open.

Inside was something that Sherlock almost wished he had never seen. There were pages and pages on Mary's past. Every job that she had been assigned as an assassin was right here in the file box. At first he assumed that they were just paper copies of whatever had been on the computer file she had given John, but then he saw the date on the most recent one. November 12, 2015. That was only a few weeks ago.

Sherlock was shocked by what was written on the page:

Date Assigned: November 12, 2015.

Name: Mary Watson Code Name: Moran.

Employer: James Moriarty

Mission: Assassinate Mycroft Holmes and Sherlock Holmes.

Sherlock heard Rosie starting to cry downstairs. He quickly put everything back the way he had found it.

"Sherlock?" Molly called.

"Yes. I'm coming," said Sherlock on his way back downstairs.

"Where were you?" she asked.

"Bathroom," Sherlock responded.

"It's your turn," Molly said with a smile as she handed over the baby.

Sherlock glared at her. "Fine."

 **A/N: Thanks for reading and Merry Christmas! I will be posting a new chapter every day until Series 4.**


	2. Chapter 2

**A/N: Six days until Series 4! Enjoy Chapter 2!**

Chapter 2:

"We're home," Mary called as she walked in the door at exactly 6:00. "How was Rosie?"

"She was wonderful, Mary," Molly said. "She didn't cause any trouble."

"Could you both stay the night? I'm exhausted," John said.

"I would love to, but I have to get home to feed Toby," Molly said. "If you ever need anything just call. Bye, Sherlock," she said, giving him a kiss on the cheek before she was out the door.

"Sherlock, would you like to stay for dinner?" asked Mary.

"Afraid I can't. I have a lot of work to catch up on," Sherlock said. He pulled John aside for a moment, "John, can I talk to you alone for a minute."

"Yeah, sure. Is everything okay?" John asked Sherlock, squinting his eyes in confusion. "We'll be back in a minute, Mary."

Once he was sure that Mary was not listening, Sherlock quickly whispered, "John, I don't quite know how to tell you this, but I don't think Mary's past is completely behind her."

"What are you talking about, Sherlock?" John said.

"I mean that she is still working as an assassin," Sherlock whispered.

"What? That's insane. Why would you even say that?" John said. "I think I would know if my wife was going around killing people."

"You didn't before," Sherlock said. He looked around the corner to make sure Mary still was not listening in before continuing. "I know this is hard to believe, but she has been hired to kill Mycroft and me."

"Why are you saying this?" John said. "Is this some kind of joke?"

"John, I'm serious. I saw the files with my own eyes right in the left room at the top of the stairs."

"Mary's office? She barely goes in there, and she keeps it locked. How would you even get in there?" John asked.

"I found the key under the angel statue," Sherlock admitted.

"So, you were just sneaking around our house while we were gone? You were supposed to be babysitting our daughter," said John, angrily.

"John, you have to believe me," Sherlock said, desperately.

Even the thought of John's wife betraying him a second time was enough to make John lose his temper. It brought back too many bad memories.

"Get out," said John.

"What?" Sherlock asked, surprised at John's reaction.

"Get out, right now."

"Why?"

"I didn't ask you to come to my house and try to ruin my marriage! Why would you even do that? Why would you even joke about something like this?"

"John, please. Mary is dangerous."

"GET OUT!"

Mary was just about to set the table for dinner when she heard Sherlock and John arguing, "What is going on in here?"

John looked at her, smiling the way he only does when he is dangerously angry. He was in kill mode. "Sherlock Holmes is not allowed back in this house alone with our daughter."

"What?" Mary said, panicked. "What happened? Sherlock, what did you do?"

"Nothing," Sherlock angrily replied before leaving the flat to catch a cab home.


	3. Chapter 3

**A/N: Five days until Series 4! Hope you enjoy Chapter 3!**

Chapter 3:

It was John's day off, so he would have the house to himself as soon as Rosie was napping. John soon became bored of watching TV. There was never anything good on at this time of day. He considered calling Sherlock to see if he needed any help on a case when he remembered the fight that they had last night.

The more he sat thinking about it, the more John became curious about what Sherlock had told him. At the time, John hadn't believed a word of it, but now he began to question why Sherlock would have made a lie up like that in the first place.

That was when John started to suspect the truth. Sherlock didn't have any reason to lie. Maybe John simply did not want to believe the truth. He suddenly snapped and decided to take a look for himself in Mary's office, not because he believed Sherlock but only because he was curious. He was glad that Sherlock had told him where the key was hidden. He had always assumed that Mary kept it with her.

He realized once he entered the room that he had no idea where Sherlock had found the information that he had told him about. He sent a text to Sherlock:

Where are the files? –JW

The wooden box. Key on top of wardrobe. –SH

There's a stool if you can't reach. –SH

John rolled his eyes, but did in fact need the stool to reach the key. He went back over the wooden box where he was stopped by the padlock.

The code? –JW

– SH

John winced at the realization of the meaning behind those letters. Could he really have been lied to a second time by Mary?

He put in the code slowly. Each letter felt like a stab to the heart. He picked up the file and started to look through the pages when he was interrupted.

"Put those down," Mary said. "Turn around."

John didn't need to be told twice. He stood up and turned to Mary who had a gun pointed right at his heart.

"Aren't you supposed to be at work today?" John asked.

"I heard you and Sherlock talking yesterday. I wanted to make sure that you didn't do exactly what you are doing right now," Mary said.

"Why are you doing this?" John asked, showing her the files in his hand.

"I didn't have a choice," Mary said, her face calm and focused.

"I thought you left this life behind," John said. "What made you change your mind?"

"I've always been like this, John. You just didn't want to believe it," Mary said. "Hand me the files."

John did as she asked, looking at the tip of the gun pointed at his heart. "Is the gun really necessary?"

"I could kill you here and now. It would make my life a lot easier."

"How can you even say that?"

"I couldn't tell you my secret, John. It would jeopardize the mission."

"What mission?"

"Moriarty wants Mycroft and Sherlock dead. They are both a threat to his plans."

"Moriarty is dead."

"The Moriarty you met is, yes, but his network is still strong at work. His legacy lives on. That's why I married you. I thought that you might know if Sherlock was still alive when he faked his death. The Holmes brothers are smart, though. They kept you in the dark."

"You don't have to do this," John said. "Just put the gun down."

"Oh, John, please don't make this more difficult than it needs to be. Now that you are aware of the situation, I need your help."

"Why would I help you?" Joh asked.

"Sherlock may be your best friend, but I am your wife."

"So, you're just going to kill him. My best friend."

"You married me."


	4. Chapter 4

**A/N: Four days until Series 4! Hope you enjoy Chapter 4! (Lots of fours. lol)**

Chapter 4:

"What do you need me to do?" asked John, accepting defeat. There was no way out of the situation so for now, he would have to at least play along.

"I'm the trained assassin so it will be easier for me to be the one to go after Mycroft with all of his government security. That leaves you with Sherlock."

John stared at her to think and then spoke, "Why would I ever agree to that?"

"He knows about my mission, but he won't expect you to do the dirty work for me. It will be easier if you go."

"Can you put that gun down now?"

Mary looked at John with suspicion before agreeing to set it on the desk next to them. John rushed at his chance to grab it and aimed it back at her.

"I suppose that was a fairly obvious trick," Mary said, echoing the words she spoke when they were at Leinster Gardens nearly a year ago. "But you would never shoot me."

"Don't be so sure. You aren't the only one who has killed people. I just need to know one thing," said John. He stood calmly with the gun in his hands. He had been trained to kill, but that wasn't his intention this time. "I still don't understand why you have to do this. There has to be a bigger motive."

"You're right. There is," Mary said. Her expression changed to one of worry. "My daughter."

"Our daughter," John corrected.

Mary nodded. "If we don't go through with this, they're going to kill Rosie."

Sherlock was relieved that John would soon discover the truth about Mary. The texts he had received from John had assured him of that. Now, he had to think of a plan to stop her. He had to warn his brother, of course. He doubted that she would only be going for an injury shot this time. Her mission stated that she had to kill both him and Mycroft.

"Mycroft?" Sherlock said over the phone.

"Yes, brother dear? What is it this time?" asked Mycroft.

"It's about Mary, but I don't think it is safe to say it over the phone. You have to come to Baker Street as soon as possible."

"It sounds serious," Mycroft said in a joking tone. "What trouble have you gotten yourself into?"

"I don't know how much time we have, but I think that both of our lives are in danger." Sherlock hung up the phone and sat down in his chair. He looked over at John's chair and thought about the sad truth that John might be spending a lot more time here at Baker Street.

It didn't take long for Mycroft to arrive at Baker Street and get filled in on all of the information he needed for his own safety. He promised Sherlock that he would work on arranging security for him as well, but he wouldn't be able to send anyone over for at least an hour. It was only a few minutes after Mycroft had left that help became necessary.

"Hello, Sherlock," John said. He wore a thick blue coat and a blue scarf similar to Sherlock's. There was still some snow on his jacket from the winter storm that had begun outside.

"John? What is it? Where is Mary?" Sherlock asked.

"I don't have a choice, Sherlock," said John as he pulled out a small silver pistol.

"Are you joking?" Sherlock asked.

"I'm sorry, Sherlock. They were going to kill Rosie."

"I already warned Mycroft. He can help. You don't have to do this."

"You were right. Mary is working for Moriarty."

"Please, John. Just put the gun down," Sherlock said, desperately.

John held his ground. He looked at Sherlock like an enemy of war. He didn't say a word as he cocked the gun and placed his finger against the trigger. He pressed his finger down, taking a single shot.


	5. Chapter 5

**A/N: Three days until Series 4, guys. I can't believe this. I'm not ready! (Enjoy Chapter 5, and sorry for yesterday's cliff hanger…not really.*evil laugh*)**

Chapter 5:

John's hands shook as he drove down an unlit street. He had come unbelievably close to betraying his best friend. But he hadn't done it. Sherlock was still alive. He had no idea whether Sherlock would have the police after him or not after this attack, but he didn't want to take any chances. John Watson was on the run for attempted murder.

He had watched people die in war before. His aim was always spot on when he was trained with a gun himself. He had even killed a man who was going to kill Sherlock, but this was different. He did not feel calm as if he had done this many times before; he was terrified.

John tried to focus on the road, but his ears were still ringing from the sound of shattered glass when he had shot the mirror behind Sherlock. It was his only chance at a distraction so that he could get back to his car and run. Now, he had to find a place to stay for the night.

Out of nowhere, a pair of headlights blinded him from his left side. A car came at him at 60 miles per hour. Before John could even comprehend the situation, glass shattered from the impact as his car was pushed off to the side of the road.

A few moments went by of stunned silence before John felt the other driver shaking him to see if he was okay. "Sir, are you alright, sir? Are you hurt?"

John looked up at the man who was moving in and out of focus. He was the last thing John saw before waking up in a hospital room.

"John? John." John opened his eyes to see his wife standing over him. "What happened, John?"

"There was a car…"

"No, not that," Mary said with a slightly annoyed tone. She had a serious look on her face with no sign of sympathy or remorse. "Did you complete the mission? Is Sherlock dead?"

John held back his gut instinct to punch this evil woman to death. Instead, he calmly answered with a lie, "Yes."

Mary was not sure if she believed him, but she nodded her head in approval.

"You should go," John said. "The police may come here to ask about the crash."

Mary looked at her husband. There was a flicker of regret in her eyes, but then it was gone. All John could see was a dark, empty stare, "Goodbye, John."

John knew that the woman who had just walked out the door was not the same woman who he had vowed to spend the rest of his life with. Whether Rosie's life had been threatened or not, if Mary had been the one standing in Baker Street that night, she would not have missed her target. The woman who John had fallen in love with ceased to exist. In fact, maybe she never had existed. Maybe, she had always been a façade.


	6. Chapter 6

**A/N: Two days, guys! Series 4 is two days away! Hope you enjoy this chapter. Only one more after this. (But an actual A/N about this chapter...) When I originally wrote this, the Sherlolly relationship was supposed to be not only an already established relationship (which it is as you will see in this chapter), but also, it was supposed to play a bigger part in the story with a lot of Sherlolly fluff. I later realized that all the Sherlolly fluff was not helping the story so I revised it, but Sherlock and Molly are still in a relationship from before this story begins and until it ends.**

Chapter 6:

Sherlock looked around at the shattered glass surrounding him. John had escaped. Sherlock couldn't call the police. John would be convicted of attempted murder. He might be let off given the circumstances, but right now, Sherlock needed to call someone he knew he could trust. The one person he had always trusted.

"Molly?"

"Sherlock? Hi, what do you need?"

"Molly, this is important. I need your help." Molly was worried. The last time Sherlock had sounded like this, he was planning to fake his own suicide.

"What do you need?" she repeated.

"I need you to come over to Baker Street right now. I'll explain everything once you are here."

"What happened in here?" Molly asked when she arrived and saw the shattered glass everywhere.

"It was John. He shot the mirror above the fireplace," Sherlock said. He was pacing around the room nervously.

"What?" exclaimed Molly.

"We don't have time to worry about that right now. John is in danger, and we need to find him."

"I don't understand. What's going on?"

"Can you drive?" Sherlock asked.

As they got in the car Molly asked where they were going. "The one place I can think of that John has to go," said Sherlock. "His sister Harry's house."

"You still haven't told me what's going on," Molly said.

"John was here only moments before I called you. He tried to shoot me," Sherlock said.

"What do you mean he tried to shoot you?" Molly asked.

"Mary has been hired by Moriarty's network to kill Mycroft and me. She sent John to kill me while she takes care of my brother. John was threatened so he didn't have a choice."

"But he missed," said Molly.

"On purpose. He shot the mirror as a distraction so that he could make a run for it. He could be miles away by now."

It took an hour and a half to reach Harry Watson's house. Sherlock knocked urgently on the door. There was no sign of John's car, but Harry might still know where John could be.

"Who are you?" asked the woman who answered the door. She clearly resembled John, and she smelled strongly of alcohol.

"I'm Sherlock Holmes, a friend of John."

"You're that detective, right? Didn't you used to be John's boyfriend?" Harry asked.

"Um," Molly cut in. "Actually, Sherlock is my boyfriend. I'm Molly by the way. He and John were never actually together."

"Not now, Molly," Sherlock whispered.

"Oh, sorry," Molly whispered back. She smiled back at Harry with her cheeks turning slightly pink.

Sherlock continued, "May we come in? We believe that John might be in danger."

Harry sighed, "I guess so."

As Sherlock and Molly walked in, they immediately noticed two empty bottles of beer next to the sofa. Harry led them into the kitchen where she offered them both a seat at the table.

"We need to know if you have gotten any calls from John or have any idea where he could be right now," Sherlock said.

"Sorry, I haven't heard anything. Is he in some kind of trouble?"

"He's on the run from the police. We don't know where he is, but we need to find him," said Sherlock.

"How do I know you aren't the police?" asked Harry.

Sherlock sighed. They weren't getting anywhere with this. He was about to suggest they leave, deciding that this had been a waste of time when the phone rang.

"I'll get it," said Harry. She went to pick up the phone.

"John's in the hospital," she said after she had hung up.

"What happened?" asked Molly.

"He was in a car crash," Harry said.

"We have to go," Sherlock said. "I'm assuming you are not coming?" he said to Harry.

"Take care of him for me," Harry said.


	7. Chapter 7

**A/N: This is the final chapter. I hope you like the ending. There is only one day left until Series 4! What are Moffat and Gatiss going to do to us?**

Chapter 7:

"John," Sherlock said, rushing over to where he was resting. His face was covered in scratches, but he didn't look seriously injured beside the fact.

The doctor, a young girl with her blonde hair pulled back in a ponytail, came in behind Sherlock. "He's going to be okay. There were no broken bones. He just needs to rest here for the night."

"It's a miracle that he wasn't more severely injured," said Molly. She saw how hurt Sherlock was to see John like this and took his hand in hers.

John woke from the noise and saw Sherlock and Molly standing nearby. He sat up quickly in his bed. "Sherlock, I told Mary that you're dead, but it won't be long before she finds out the truth. You aren't safe here."

"I'm going to call Mycroft to find Mary and protect Rosie. It's okay. Everyone is safe," Sherlock said.

"No it's not! I almost killed you!" John shouted.

Sherlock's voice remained calm, "But you didn't."

"I think you should let him rest now," the doctor said.

After a few calls, Mycroft confirmed with Sherlock that everything had been taken care of. Mary was found in a car parked outside Mycroft's main government building. She was arrested and immediately thrown in prison to be tried for attempted murder and treason. Rosie was put under protection with high security.

Once John had fully recovered, Sherlock went with him to the prison where Mary was. They were taken to a room where John sat down and could speak to Mary behind bars. They stared at each other in silence with Sherlock watching behind John,

John looked at his wife with an angry smile. "How did I not see this coming?" he asked her.

Mary looked at him without saying a word.

"Why did you keep your secret from me?"

Again, she said nothing. John stood up from his chair.

"Why did you force me to shoot my best friend? Why did you put our daughter in danger! Why did you betray me! Why did you lie to me! That's all you are! A liar!"

Her expression remained unchanged.

"John, let's go," Sherlock said.

John had one last look at Mary Watson before he followed Sherlock out of the room.

"Why did she have to be like this?" John asked Sherlock. "She wasn't supposed to be like this."

Sherlock responded, "Because…you chose her."

 **A/N: Happy Sherlock Eve! If this tragic ending was too much, and you want a happy epilogue, let me know. I might start working on a Johnlock one shot now to get even more excited than I already am for this series finale (I believe in TJLC!).**

 **Also, if you have not seen the video that inspired this fic by BeautifullyTragic6 "Detective vs Assassin", go watch it on YouTube. Thanks again, Beauty. You're the best.**


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